Taxonomic distribution of proteins containing Bac_rhodopsin domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing Bac_rhodopsin domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Electron-crystallographic refinement of the structure ofbacteriorhodopsin.

Grigorieff N, Ceska TA, Downing KH, Baldwin JM, Henderson R
J Mol Biol. 1996; 259: 393-421

Using electron diffraction data corrected for diffuse scattering togetherwith additional phase information from 30 new images of tilted specimens,an improved experimental density map has been calculated forbacteriorhodopsin. The atomic model has then been rebuilt into this newmap with particular attention to the surface loops. All the residues from7 to 227 as well as ten lipid molecules are now included, although a fewamino acid residues in three of the six surface loops, about half of thelipid hydrophobic chains and all of the lipid head groups are disordered.The model has then been refined against the experimental diffractionamplitudes to an R-factor of 28% at 3.5 angstrom resolution with strictgeometry (0.005 angstrom) bond length deviation) using the improvement ofthe "free" phase residual between calculated and experimental phases fromimages as an objective criterion of accuracy. For the refinement some newprograms were developed to restrain the number of parameters, to becompatible with the limited resolution of our data. In the final refinedmodel of the protein (2BRD), compared with earlier co-ordinates (1BRD),helix D has been moved towards the cytoplasm by almost 4 angstrom, and theoverall accuracy of the co-ordinates of residues in the other six heliceshas been improved. As a result the positions of nearly all the importantresidues in bacteriorhodopsin are now well determined. In particular, theburied, protonated Asp115 is 7 angstrom from, and so not in contact with,the retinal and Met118 forms a cap on the pocket occupied by thebeta-ionone ring. No clear density exists for the side-chain of Arg82,which forms a central part of the extracellular half-channel. The onlyarginine side-chain built into good density is that of Arg134 at theextracellular end of helix E, the others being disordered near one of thetwo surfaces. The interpretation of the end of helix F on theextracellular surface is now clearer; an extra loose helical turn has beenbuilt bringing the side-chain of Glu194 close to Arg134 to form a probablesalt bridge. The model provides an improved framework for understandingthe mechanism of the light-driven proton pumping. A number of cavitiesthat could contain water molecules were found by searching the refinedmodel, most of them above or below the Schiff base in the half-channelsleading to the two surfaces. The ordered and disordered regions of thestructure are described by the temperature factor distribution.

Primary structure of sensory rhodopsin I, a prokaryotic photoreceptor.

Blanck A, Oesterhelt D, Ferrando E, Schegk ES, Lottspeich F
EMBO J. 1989; 8: 3963-71

The gene coding for sensory rhodopsin I (SR-I) has been identified in arestriction fragment of genomic DNA from the Halobacterium halobium strainL33. Of the 1014 nucleotides whose sequence was determined, 720 belong tothe structural gene of SR-I. In the 5' non-coding region two putativepromoter elements and a ribosomal binding site have been identified. The3' flanking region bears a potential terminator structure. The SR-Iprotein moiety carries no signal peptide and is not processed at its Nterminus. The C terminus, however, lacks the last aspartic acid residueencoded by the gene. Analysis of the primary structure of SR-I reveals noconsistent homology with the eukaryotic photoreceptor rhodopsin, but 14%homology with the halobacterial ion pumps, bacteriorhodopsin (BR) andhalorhodopsin (HR). Residues conserved in all three proteins are discussedwith respect to their contribution to secondary structure, retinal bindingand ion translocation. The aspartic acid residue which mediates in BR thereprotonation of the Schiff base (D96) is replaced in SR-I by a tyrosine(Y87). This amino acid replacement is proposed to be of crucial importancein the evolution of the slow-cycling photosensing pigment SR-I.

Two pumps, one principle: light-driven ion transport in halobacteria.

Oesterhelt D, Tittor J
Trends Biochem Sci. 1989; 14: 57-61

Comparison of the primary structure of the chloride pump halorhodopsinwith that of the proton pump bacteriorhodopsin provides insight intolight-driven ion transport by retinal proteins. Several conserved aminoacid residues in the membrane-spanning region of both proteins and theirinteraction with different isomerization states of retinal are suggestedto be the key element for ion transport in both proteins.